4/4/2001 2:00 PM
4/6/2001 4:00 PM
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The international agreement discussed at the Airlie meeting called for releasing structure information on most proteins soon after completion but setting aside some structures for a limited period of time (less than 6 months) to allow for application for patents. However, the NIGMS has a more stringent policy. As stated in the
Request for Applications, NIGMS Protein Structure Initiative (PSI) grantees are required to make timely deposition of structural coordinates and related data into a public database upon completion of the atomic structure.
The NIH research centers are just getting under way, and it is unclear how much time is needed to ensure that the results are accurate and to prepare the results for publication and deposition in the Protein Data Bank. The PSI program's current policy is to limit this time to 4 to 6 weeks. This should also be adequate time for the investigators to file patent applications for protein structures of commercial interest.
John C. Norvell
Director, Protein Structure Initiative
National Institute of General Medical Sciences
45 Center Drive, Room 2AS.13B
Bethesda, MD 20892-6200
As the human genome sequence is being completed, scientists have begun a large-scale project to determine the three-dimensional shapes of all proteins and other important biomolecules encoded by the genomes of key organisms. The project, called structural genomics, will provide a basis for modeling how life works in molecular detail, with important applications in medicine and biotechnology. The structural genomics community, with participants from four continents, passed an international collaborative agreement at the Second International Structural Genomics meeting held April 4-6, 2001, at Airlie Conference Center near Washington, D.C.
'Airlie Agreement' provides for open sharing of scientific data and technological expertise. The agreed conditions for the sharing of data reflect the balance between two different goals -- timely release of all structural genomics data to the public and consideration for intellectual property regulations that vary significantly in different countries. For projects with public funding, all data on biomolecular shapes are to be made available to the public in all countries soon after their determination. In addition, the agreement recognized the potential for collaboration between structural genomics researchers in academia and in industry. The Airlie Agreement extends and refines an earlier agreement reached in April 2000 at the First International Structural Genomics meeting on the Wellcome Trust Genome Campus near Cambridge, UK.
Specifically, the Airlie meeting reached general agreement on international collaboration in a number of areas, including standards for early data release, criteria for assessing the quality of structures, the sharing of targeted proteins lists, and the archiving and curation of all data:
*General agreement on rapid release of data and wide availability to the international public
*For projects with public funding:
* Obtaining high quality structures is of primary importance. Projects must not compromise quality for high throughput operation.
* It is the responsibility of the investigator to make certain that sufficient quality is reached.
* Structural genomics laboratories with public funding have agreed to adopt a policy of open exchange of target information.
* Because patent laws vary between different countries and are unclear regarding the products of structural genomics, the meeting participants encourage patent offices and courts to harmonize the laws. They also welcome strengthened utility conditions for inventions based on these structures.
* The group elected an executive committee to establish an international organization for structural genomics and to plan the next international meeting. This committee consists of Tom Terwilliger (U.S.), Udo Heinemann (Europe), and Shigeyuki Yokoyama (Japan).
The meeting participants also shared their experiences and problems setting up large-scale, high throughput structural genomics operations. Many of the groups gave brief presentations on the highlights and status of their projects.
What is structural genomics?
The structural genomics project is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. The effort builds on the information of the genome sequencing projects. While gene sequencing determines the information content of entire genomes, structural genomics seeks to determine the molecular shapes of the complete set of cellular components that make life work. Knowledge of these three-dimensional shapes teaches us how cells and organisms function. Structural genomics has applications in the life sciences, biotechnology, and medicine, where it can serve as a basis for the development of medications, vaccines, and diagnostics.
The field of structural genomics has developed over the last 3 years and now is reaching significant dimensions. It builds on a long tradition of structural biology, in particular X-ray crystallography, nuclear magnetic resonance (NMR) and computational model building. It is now aiming at high throughput operations and complete coverage of the universe of protein structures.
Currently, there is significant funding for structural genomics projects in the U.S., Canada, the European Union, Israel, China, and Japan. The Airlie meeting was funded by the National Institute of General Medical Sciences , a component of the U.S. National Institutes of Health; the
Wellcome Trust, a UK-based medical research charity; and R?IKEN (a public corporation of the Japanese government) MEXT (Ministry of Education, Culture, Sports, Science and Technology).
This document reports the principles agreed at the April 4-6, 2001 meeting of representatives of the structural genomics community. Its purpose is to generate further co-operation in the structural biology and general scientific communities.
This Airlie Agreement builds on the agreement produced following the first international meeting in Hinxton, UK, in April 2000. The broad overall goals and principles are unaltered. Policy extensions and more detailed definitions are based on the initial reports of the five task forces that were established following the first meeting, and discussions at the second meeting. The amended reports of the task forces are included at the end of this document.
The field of structural genomics continues to evolve very rapidly, and it is expected that further policy revisions in many areas will be made at subsequent meetings of the community.
Success of the genome sequencing projects and major advances in methods of protein structure determination have led the structural biology community to propose the large scale mapping of protein structure space. This structural genomics initiative aims at the discovery, analysis and dissemination of three-dimensional structures of protein, RNA and other biological macromolecules representing the entire range of structural diversity found in nature. Such a complete knowledge will facilitate fundamental understanding and applications in biology, agriculture and medicine. The three-dimensional structures will be crucial for rational drug design, for advancing catalysis in chemistry and biotechnology, and for diagnosis and treatment of disease, as well as for advancing basic principles of biology. A broad collection of structures will provide valuable biological information beyond that which can be obtained from individual structures.
This opportunity is made possible by rapid progress in several related key technologies. These include the construction of synchrotrons and high-field NMR instruments, the MAD method of phase determination, high throughput cloning and recombinant expression, a flood of information from genome sequencing projects, and bioinformatic methods for fold assignment, model building, and prediction of function.
The following document outlines issues related to achieving this expansion of knowledge. The goal is to encourage harmonious cooperation among a broad range of public and private sector institutions in the international effort to characterize macromolecular structures in living organisms on a pan-genomic scale.
Raw fundamental data on the shape of natural protein molecules, including 3D positional coordinates, should be made freely available to researchers everywhere. However, intellectual property protection for inventions based on these can play an important role in stimulating the development of important new health care projects.
Public funding for structural genomics has varying degrees of support for fundamental science and for potential commercial exploitation. The data release policy described earlier has been designed to accommodate these differences, at the same time optimizing the speed of release of data as much as possible under all circumstances.
Fundamental research underpins all practical uses and applications. Policy makers are urged to preserve and promote the free access and exchange of scientific information among scientists engaged in basic research. This community welcomes efforts around the world to harmonize patent law.
We also encourage efforts to strengthen the utility requirement for patentability. This community is concerned about the implications of the granting of patents based solely on the submission of three-dimensional structural co-ordinates, without any identified non-trivial utility.
Further meetings of representatives of the structural genomics community are anticipated for the continued reexamination of these issues and to further develop these principles and guidelines as the field expands and evolves. The next meeting will occur in Berlin, Germany in October 2002.
These principles were supported by the participants in the Second International Structural Genomics Meeting in the Airlie Center, Virginia, USA, April 4-6, 2001.
Day 1 - Wednesday, April 4:
Welcome John Norvell
Agency Perspectives NIH Marvin Cassman Wellcome Trust Barbara Skene MEXT Toichi Sakata
Introduction John Moult & Chris Sander
International Organization Tom Terwilliger
3:45 - 5:15 pm
Report of the Task forces (1) Chair: Joel Janin Data Capture Helen Berman Target Tracking Steve Bryant Data Quality Assurance Randy Read
5:15 - 5:45 pm Tea/coffee
5:45 - 6:45 pm
Project Bottlenecks (1) Chairs: Wayne Hendrickson Michal Linial William Studier Report from active groups: what are the biggest technical challenges?
6:45 - 8:45 pm Drinks and dinner
8:45 - 10:15 pm
Relations between Industry and Academia Chair: Dino Moras The Structural Genomics Consortium Barbara Skene Views of a CEO of a structural genomics company Tim Harris
Day 2 - Thursday, April 5:
7:00 - 8:30 am Breakfast 8:30 - 9:15 am
Intellectual Property Rights Chair: Joel Sussman Intellectual property issues for structural genomics Joseph Straus
9:15 - 10:00 am
Report of the Task forces (2) (continued) Chair: Stephen Burley Intellectual Property Rights Marvin Cassman/John Norvell Publication Guy Dodson
10:00 - 10:30 am Coffee/tea 10:30 - 11:30 am
Project Bottlenecks (2)
(continued) Chairs: Wayne Hendrickson, Michal Linial,
11:30 - 12:30 pm
Review draft agreement/policy document
12:30 - 2:00 pm Lunch
2:00 - 3:30 pm
Bottlenecks (1) Chair: Shigeyuki Yokoyama cDNA repository Josh Labaer Automation of NMR structure determination
and refinement Michael Nilges
3:30 - 4:30 pm
Policy Discussion Discuss revisions to policy document
4:30 - 5:00 pm Tea/coffee
5:00 - 7:00 pm Parallel sessions
(1) Highlights from structural genomics groups Chair: Ivano Bertini
(2) Work groups to revise draft agreement / policy document
7:00 - 8:30 pm Drinks and dinner
8:30 - 10:00 pm
Pass draft agreement / policy document
Day 3 - Friday, April 6:
7:00 - 8:30 am Breakfast
8:30 - 10:30 am
Bottlenecks (2) Chair: Udo Heinemann Miniaturization of protein production and crystallization Ian Wilson Automation of crystal structure solution and refinement Tom Terwilliger Comprehensive functional characterization of gene products Lee Makowski
10:30 - 11:00 am Coffee/tea
11:00 - 12:30 pm
Pass final consensus agreement and dissemination plan
12:30 pm Lunch
Formal close of meeting
1:30 - 4:00 pm Working groups as needed to polish final policy document & press release
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